Tagged Questions

Bioinformatics connects life sciences and quantitative sciences, typically involving the application of software and algorithms to solve computationally intensive questions, such as those in genomics, sequence analysis, and systems biology. Questions tagged Bioinformatics should have a direct ...

I'm working with data downloaded from STRING database (string-db.org) for protein-protein interactions.
My idea is to compare the topology of connections of the same protein on different organisms.
...

I am looking for a large collection (>1000) of sequence files (eg. FASTA) from any real organism or a tool to create such a collection.
The sequence files would be used for teaching and for testing ...

Almost all of the papers about bioinformatics, I faced with the high-throughput word, but I could not find any explanation about it (I think it is so easy to understand and thats why anyone explains ...

I have a list of ENA accession numbers and a start and end position in each sequence. In the end I want to align all those sequences, but first I have to fetch them and the list is too long to do that ...

I understand that one can translate a nucleotide sequence and run PSI-BLAST on the protein (proteins if you take the 6 reading frames), but I'm looking for distant homology for bacterial small RNAs ...

I was doing some gene expression analysis using this tool http://david.abcc.ncifcrf.gov/summary.jsp. However, I have a confusion about what benjamini is. I fed it some gene list and it gave me some ...

Is there any evidence showing that copy number variation changes over time? I'm wanting to model interactions in expression level as a dynamic bayesian network, but an assumption my approach will need ...

I am searching E.coli whole genome expression data with different conditions, any suggestion is appreciated. Condition could be for example different growth temperature, different medias, etc.
I have ...

Which algorithm or algorithms are considered the standard or state-of-the-art for multiple sequence alignment?
How big is the need for better algorithms? How many sequences need to be alignment in a ...

I'm studing for my bachelor's degree in Natural Science and I have to chose the path for my future life. I have to chose the right kind of graduate studies. Since I love computer science, maths and ...

There are many hydrophobicity scales for protein analysis.
Broadly, I gather the differences between them are from the experimental method to acquire the data and the normalisation (or lack thereof) ...

I understand that many curated trees of life already exist (eg http://tolweb.org/tree/) but is there any website that allows one to input a list of organisms, and then produce the current best guess ...

I am trying to find a version of the BLOSUM matrix that has the frequencies instead of the scaled log-odds. i.e. instead of the common version that tells us that the score LEU/ASP is -4, I would like ...

In a standalone blast search, is there a parameter that could be specified to fix the number of mismatches allowed in an alignment. I went through the parameters and I could only find parameters to ...

I have a list of differentially expressed genes from an RNA-Seq experiment in Xenopus laevis that I'm looking to functionally annotate with GO-terms. As X.laevis is not listed in DAVID it seems I have ...

I have a set of gene expression data downloaded from http://www.ncbi.nlm.nih.gov/geo. I have two sets of data, one is the raw probe intensity data set in the form of CEL files. Another is processed ...

I am trying to calculate a log-odds matrix for MAST input, from a position-specific probability matrix for the motif in which I am interested.
I would like to know how MEME estimates the background ...

Is there any software that could be used to rapidly (quicker than humans) count the eggs laid by Drosophila on a substrate by placing them under a microscope with a camera attached? The eggs are laid ...

I need to draw a map of the core metabolism of E.coli. Associated with each reaction in the map I have a number that indicates the flux through this reaction. I want the map to reflect these fluxes ...

My short term goal in a project is to build a local database of the NCBI dbSNP database. The data and schema are available on the FTP site(). I was going to implement the database using MySQL, but I ...

I was rooting through the literature, but there is too much work on the topic of detecting loops in RNA and the RNA helices that go with them. Can anyone point to a good review on this topic or even ...